A voyage into the unknown that conjures more questions than it answers … That's what we were told to expect from Ridley Scott's long-awaited sort-of-Alien-prequel Prometheus, with a script by Lost writer Damon Lindelof. We thought they were talking about the characters' journey into the depths of space to meet the extraterrestrial originators of life on earth. It turned out, though, to refer to us poor lugs in the audience, stumbling out into the night scratching our heads. Here we try to untangle some of the film's more prominent puzzlers. Spoilers abound, of course, and we're frankly as stumped as you - so do chip in in the comments …

1. What's going on in the prologue? That's an alien creating life on earth, right?

Um… probably? That certainly seems to be the case: we see an engineer, apparently left alone on a barren earth as his fellows ship out, who consciously sacrifices himself by drinking black goo that causes his body to crumble into little bits of DNA that spread throughout the world. But as they look much like the engineers our heroes encounter, wouldn't that mean their biology and technology hasn't changed in billions of years? Perhaps this can be filed under 'things Ridley Scott wants us to wonder about' – he has talked about ideas for a sequel engaging with the engineers' motivations more directly.

2. How did the constellation get onto all those ancient cave paintings and artefacts? And why would the engineers provide a map anyway?

They're too recent for the engineers to have left them when they created life – did they somehow appear to humans in visions? Were they based on engineer artefacts that haven't survived? Have the engineers been popping back every so often? And given their later hostility, why would the engineers want to leave directions anyway? Was it a test? Or an alarm designed to notify them of mankind's development of space travel?

3. Why would a crew of off-the-street technicians and world-renowned scientists take a years-long trip into deep space without knowing what they were getting themselves into?

File under 'movie characters do dumb shit'. Prometheus is full of moments in which characters' motivations are unclear or absurd and it's probably not worth dwelling on them beyond recognising that, well, the script is very patchy. See also: Why wouldn't the crew check out the alien landscape before exploring unarmed? Why would they remove their helmets in an alien atmosphere? Why would they plunge their fingers in alien goo or try to pet an alien snake monster? Why wouldn't you run sideways when a wheel-shaped spaceship is rolling towards on you? We could go on.

4. Why does the black goo affect different people in different ways?

Contact with the alien goo seems to have a range of effects: the engineer at the beginning more or less crumbles to dust; it seems to cause worms to mutate into snakelike creatures; one crew member becomes a marauding zombie-like monster while another apparently absorbs the substance into his DNA, resulting in Elizabeth being impregnated with what seems to be a rudimentary facehugger, which somehow grows to enormous size and then impregnates an engineer with what turns out to be a rudimentary Alien… It's all awfully muddled. The most charitable conclusion is that this is seriously protean stuff capable of speedy adaptation to suit whatever environment and host it comes across.

It seems bonkers to cast a young man as an old man – it's not as if Ridley Scott was short of options for the older gentleman and Pearce spends the whole movie clad in prosthetic wrinkles. Well, the movie, yes – but not Prometheus's viral campaign, which saw Pearce giving a TED talk as the younger Peter Weyland. That seems a relatively small reason to influence the casting of the film itself, but perhaps Scott is keeping his options open for flashback sequences in a possible sequel?

6. Why is Weyland so cagey about revealing himself?

It's his ship and his expedition, after all – and even if he wanted to keep his involvement secret ahead of time, why not reveal his presence to his employees once they'd been woken from hypersleep? It's not like they'd be going anywhere. Perhaps he just doesn't like socialising?

7. Why did David drop the goo into Holloway's drink?

It seems somewhat rash of David the android to deliberately infect one of his fellow crew members with alien goo. Is he just working out the robo-resentments he seems to nurse against his human fellow travellers? It seems more likely that this is part of Weyland's plan to harness the power of the goo in the service of his own immortality. If so, Holloway's fate offers a pretty good reason to hold off.

8. How was Elizabeth running around minutes after a self-administered emergency Caesarean?

Even by the standards of science fiction, the idea of someone having their belly sliced open while conscious, watching the removal of a baby-sized squid monster, getting stapled up and immediately being in fit shape to barrel around, running and fighting, is outlandish. It seems impossible that the filmmakers didn't realise this, yet no obvious excuse is offered. Does the miracle medicine pod double as some kind of strength-endowing, pain-suppressing supercharger?

9. Why did the engineers change their minds and decide to destroy life on earth?

This is certainly one of the known unknowns that Scott and Lindelof are concealing in expectation of a sequel. If we're right that the engineers created life on earth, why would they now want to destroy it? Could it be that old chestnut about mankind evolving to the stage of being a threat to other lifeforms in the universe? A friend of mine suggests that the engineer from the prologue was in fact a rogue operator whose fellow engineers are belatedly trying to undo his handiwork – a neat theory that resonates with the original Prometheus myth.

10. Isn't it all a bit X-Files-y?

Ancient extraterrestrials kick-start life on earth with some sort of apparently animate black goo as its vehicle; humans decode signs from ancient and indigenous art and artefacts; there are big round spaceships buried underground that heave out of the earth at inopportune moments; super-rich, super-selfish humans try to manipulate the situation for their own gain even as the fate of mankind is in jeopardy … Much of this will be familiar to viewers of The X-Files – who will probably have been grateful for something familiar to orient themselves around amid all the other uncertainties. As for whether the truth about Prometheus is out there, we'll have to watch the skies. Or at least the box office for the prospect of a sequel …